Genomics stands at a remarkable moment of scientific opportunity and technological ferment. DNA sequence information is becoming an increasingly powerful for investigating biological question, and new technologies promise to decrease dramatically the cost of DNA sequencing and thereby further expand its reach. At the same time, the scientific and technological path forward has many uncertainties and obstacles. For these reasons, NHGRI seeks to support genome centers with the ability to provide both scientific and technological leadership through this exciting period of transition. This proposal has three specific aims: Aim 1. Current technology. We propose to operate a state-of-the-art genome center using current sequencing technology, continuing our 15-year track record of high throughput, low cost and flexibility. Our annual throughput will exceed 61 billion bases, with costs decreasing to $0.29/kQ20 base by the end of Year 4. The capacity will have the potential to be allocated flexibly across shotgun sequencing, targeted sequencing and finishing/improvement. Aim 2. New technology. In parallel, we aim to completely replace the current generation with new, disruptive technologies, with the goal of dramatically decreasing cost and increasing output. During the first year, we will operate two new sequencing platforms (454 and Solexa) at sufficient scale to understand their true performance, cost and utility and to produce valuable data. Based on the results, we aim to scale-up one or both platforms as soon as possible. This work requires more than simply implementing new instruments at production scale, although this is a substantial challenge. The greater challenge is that the two platforms are not currently suited to NHGRI's key genomic applications [unreadable] namely, genome assembly and directed re-sequencing. We will develop the full set of laboratory and computational tools required to adapt the technologies to these key applications. Our goal will be to achieve a cost reduction of >30-fold in these key applications by the end of the grant period. Aim 3. Scientific leadership. We will continue to serve as an intellectual resource for the scientific community, by pioneering new approaches for using DNA sequence to solve important biomedical problems and by working with the community to rapidly disseminate ideas, methods and data.